Rocketman,
If you were to save the Nav Data from your Humminbird to the SD card and load them into HumminbirdPC it will treat it as a separate file or group of data. Try it using the Point of Sale Simulator (power cable only attached) by saving some waypoints and exporting them to the SD card. When you download them in Humminbird PC you will notice that they will come up in a different file on the left side of the screen.
Now if you were to make changes to these same waypoints, upload them back to the SD card (replacing the data on the SD card), than load them into your Humminbird unit – you will have duplicate waypoints. In my opinion; the best way to handle this would be to export the Nav Data to the SD card, save it in HumminbirdPC (with some sort of date code in the file name like Eufaula_09.21.09.gpx), go back and Delete All Nav Data from your Humminbird unit, make the changes you want to the Nav Data now in HumminbirdPC, than upload it back to the SD card (replacing the data that is there) and loading the SD card back into your Humminbird where only the data you loaded onto the SD will be on your Humminbird unit.
Some folks here are working on some videos and such that will help with HumminbirdPC and some of the menu features in the unit.